Fig 1.
Structure of the NiV nucleocapsid protein-RNA complex.
CryoEM structure of the nucleocapsid complex, determined at 3.5 Å resolution. Two orthogonal views of the CryoEM map (left) are shown next to the corresponding molecular models (right). (B) Schematic representation of the nucleocapsid protein, with the colour-coding as in (A). Boxed segments correspond to regions with defined structure. Dashed line corresponds to the disordered region.
Fig 2.
Protomer-protomer interactions within the NiV nucleocapsid assembly.
(A) Three adjacent protomers, where the two outside protomers are presented as ribbons and the central protomer is shown in surface representation, with the NT-arm in blue, N-terminal Ncore in green, C-terminal Ncore in coral and CT-arm in grey, as in Fig 1B. A magnified view of the molecular interaction of the NT-arm and the C-terminal Ncore domain is shown on the right with interacting residues (sticks) displayed within the CryoEM map. (B) The P protein segment from the structure of the complex with the monomeric NiV N form (yellow ribbon, pdb:4co6)[15] superimposed onto the central subunit in (A), shown in white surface representation. The two adjacent protomers are presented as dark-blue (n+1) and red (n-1) ribbons. (C) Alignment of interacting residue segments, shown in the magnified view in (A), for N proteins from several Paramyxoviruses, with conserved residues highlighted using the ClustalX colour scheme.
Fig 3.
(A) Three adjacent protomers shown as in Fig 2A, with RNA (purple) shown in ribbon and sticks. (B) CryoEM map corresponding to the RNA, with a fitted poly-uridine RNA model (sticks). (C-D) Two different views at the protein-RNA interface, detailing protein-RNA interactions. CryoEM density corresponding to the side chain atoms of interacting residues, is shown with a 3 Å distance cut-off. (E) Alignment of RNA-binding residue segments from several Paramyxoviral N proteins with conserved residues highlighted using the ClustalX colour scheme. (F) Schematic of the ssRNA conformation in complex with the N protein. The residues in close proximity to RNA are labelled. Boxed residues indicate those from the neighbouring protomer; the blue dotted lines indicate putative hydrogen bonding interactions; red curves indicate putative hydrophobic interactions.
Fig 4.
Mapping sequence variation to the structure.
The surface of the NiV nucleocapsid assembly is coloured according to sequence conservation among Paramyxoviral N proteins based on ConSurf analysis, visualised at three different orientations. Inset (bottom right) compares the conformation of the residue segment 118–139 containing helix H5, in four different Paramyxoviruses: NiV, Parainfluenza virus 5 (PIV5, PDB code 4xjn), Newcastle Disease virus (NDV, PDB code 6jc3) and Measles (PDB code 6h5q).
Fig 5.
Clam-shaped nucleocapsid assembly.
(A) Model of the clam-shaped nucleocapsid assembly, presented as a molecular surface with subunits coloured as in Fig 2A, showing the interaction between two opposing, top and bottom N protein spirals, with one of the protomers shown as ribbon. (B) The clam-shaped interaction is primarily mediated by protein loops from the N-terminal Ncore domain. Putative residues involved in the interaction between the two halves of the shell are indicated. (C) Alignment of the three interacting loop regions highlighted in (B) for N proteins from several Paramyxoviruses, with glycine, proline and surrounding conserved residues highlighted using the ClustalX colour scheme.
Fig 6.
Phylogenetic relation of the N protein within the Mononegavirales.
(A) Phylogenetic tree based on the N protein sequences of selected Mononegavirales. N proteins with available protein structures are coloured in red. (B) RNA binding region of Nipah virus, Ebola virus, Respiratory Syncytial Virus, and Vesicular Stomatitis Virus showing the conserved protein-RNA interaction among these viruses. Residues involved in protein-RNA interactions are shown as sticks.